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ERC000017.json
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ERC000017.json
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{"id": "ERC000017", "dataTypeId": "samples", "displayName": "GSC MIxS human skin", "description": "Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.", "spreadsheetTemplate": {"columnCaptures": {"alias": {"fieldName": "alias", "fieldType": "String", "required": true}, "title": {"fieldName": "title", "fieldType": "String", "required": true}, "description": {"fieldName": "description", "fieldType": "String", "required": false}, "release date": {"fieldName": "releaseDate", "required": true}, "taxon": {"fieldName": "taxon", "fieldType": "String", "required": true}, "taxon id": {"fieldName": "taxonId", "fieldType": "IntegerNumber", "required": true}, "project name": {"required": true, "allowUnits": false, "allowTerms": false}, "experimental factor": {"required": false, "allowUnits": false, "allowTerms": false}, "ploidy": {"required": false, "allowUnits": false, "allowTerms": false}, "number of replicons": {"required": false, "allowUnits": false, "allowTerms": false}, "extrachromosomal elements": {"required": false, "allowUnits": false, "allowTerms": false}, "estimated size": {"required": false, "allowUnits": false, "allowTerms": false}, "reference for biomaterial": {"required": false, "allowUnits": false, "allowTerms": false}, "finishing strategy": {"required": false, "allowUnits": false, "allowTerms": false}, "annotation source": {"required": false, "allowUnits": false, "allowTerms": false}, "sample volume or weight for DNA extraction": {"required": false, "allowUnits": false, "allowTerms": false}, "nucleic acid extraction": {"required": false, "allowUnits": false, "allowTerms": false}, "nucleic acid amplification": {"required": false, "allowUnits": false, "allowTerms": false}, "library size": {"required": false, "allowUnits": false, "allowTerms": false}, "library reads sequenced": {"required": false, "allowUnits": false, "allowTerms": false}, "library construction method": {"required": false, "allowUnits": false, "allowTerms": false}, "library vector": {"required": false, "allowUnits": false, "allowTerms": false}, "library screening strategy": {"required": false, "allowUnits": false, "allowTerms": false}, "target gene": {"required": false, "allowUnits": false, "allowTerms": false}, "target subfragment": {"required": false, "allowUnits": false, "allowTerms": false}, "pcr primers": {"required": false, "allowUnits": false, "allowTerms": false}, "multiplex identifiers": {"required": false, "allowUnits": false, "allowTerms": false}, "adapters": {"required": false, "allowUnits": false, "allowTerms": false}, "pcr conditions": {"required": false, "allowUnits": false, "allowTerms": false}, "sequencing method": {"required": true, "allowUnits": false, "allowTerms": false}, "sequence quality check": {"required": false, "allowUnits": false, "allowTerms": false}, "chimera check": {"required": false, "allowUnits": false, "allowTerms": false}, "relevant electronic resources": {"required": false, "allowUnits": false, "allowTerms": false}, "relevant standard operating procedures": {"required": false, "allowUnits": false, "allowTerms": false}, "investigation type": {"required": true, "allowUnits": false, "allowTerms": false}, "collection date": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (country and/or sea)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (latitude)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (longitude)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (region and locality)": {"required": false, "allowUnits": false, "allowTerms": false}, "human skin environmental package": {"required": true, "allowUnits": false, "allowTerms": false}, "environment (biome)": {"required": true, "allowUnits": false, "allowTerms": false}, "environment (feature)": {"required": true, "allowUnits": false, "allowTerms": false}, "environment (material)": {"required": true, "allowUnits": false, "allowTerms": false}, "source material identifiers": {"required": false, "allowUnits": false, "allowTerms": false}, "sample collection device or method": {"required": false, "allowUnits": false, "allowTerms": false}, "sample material processing": {"required": false, "allowUnits": false, "allowTerms": false}, "isolation and growth condition": {"required": false, "allowUnits": false, "allowTerms": false}, "propagation": {"required": false, "allowUnits": false, "allowTerms": false}, "amount or size of sample collected": {"required": false, "allowUnits": false, "allowTerms": false}, "host body product": {"required": false, "allowUnits": false, "allowTerms": false}, "medical history performed": {"required": false, "allowUnits": false, "allowTerms": false}, "oxygenation status of sample": {"required": false, "allowUnits": false, "allowTerms": false}, "organism count": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage duration": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage temperature": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage location": {"required": false, "allowUnits": false, "allowTerms": false}, "dermatology disorder": {"required": false, "allowUnits": false, "allowTerms": false}, "host disease status": {"required": false, "allowUnits": false, "allowTerms": false}, "host subject id": {"required": false, "allowUnits": false, "allowTerms": false}, "IHMC medication code": {"required": false, "allowUnits": false, "allowTerms": false}, "host age": {"required": false, "allowUnits": false, "allowTerms": false}, "host body site": {"required": false, "allowUnits": false, "allowTerms": false}, "host height": {"required": false, "allowUnits": false, "allowTerms": false}, "host body-mass index": {"required": false, "allowUnits": false, "allowTerms": false}, "IHMC ethnicity": {"required": false, "allowUnits": false, "allowTerms": false}, "host occupation": {"required": false, "allowUnits": false, "allowTerms": false}, "host total mass": {"required": false, "allowUnits": false, "allowTerms": false}, "host phenotype": {"required": false, "allowUnits": false, "allowTerms": false}, "host body temperature": {"required": false, "allowUnits": false, "allowTerms": false}, "host sex": {"required": false, "allowUnits": false, "allowTerms": false}, "temperature": {"required": false, "allowUnits": false, "allowTerms": false}, "sample salinity": {"required": false, "allowUnits": false, "allowTerms": false}, "miscellaneous parameter": {"required": false, "allowUnits": false, "allowTerms": false}, "time since last wash": {"required": false, "allowUnits": false, "allowTerms": false}, "dominant hand": {"required": false, "allowUnits": false, "allowTerms": false}, "host diet": {"required": false, "allowUnits": false, "allowTerms": false}, "host last meal": {"required": false, "allowUnits": false, "allowTerms": false}, "host family relationship": {"required": false, "allowUnits": false, "allowTerms": false}, "host genotype": {"required": false, "allowUnits": false, "allowTerms": false}, "host pulse": {"required": false, "allowUnits": false, "allowTerms": false}, "subspecific genetic lineage": {"required": false, "allowUnits": false, "allowTerms": false}, "trophic level": {"required": false, "allowUnits": false, "allowTerms": false}, "relationship to oxygen": {"required": false, "allowUnits": false, "allowTerms": false}, "known pathogenicity": {"required": false, "allowUnits": false, "allowTerms": false}, "encoded traits": {"required": false, "allowUnits": false, "allowTerms": false}, "observed biotic relationship": {"required": false, "allowUnits": false, "allowTerms": false}, "chemical administration": {"required": false, "allowUnits": false, "allowTerms": false}, "perturbation": {"required": false, "allowUnits": false, "allowTerms": false}}, "defaultCapture": {"required": false, "allowUnits": false, "allowTerms": false}}, "version": 1, "new": true, "validationSchema": {"version": "1.0.0", "author": "ENA", "definitions": {"attribute": {"type": "array", "minItems": 1, "items": {"required": ["value"], "properties": {"value": {"minLength": 1, "type": "string"}, "terms": {"$ref": "#/definitions/terms"}, "units": {"minLength": 1, "type": "string"}}}}, "terms": {"type": "array", "items": {"required": ["url"], "type": "object", "properties": {"url": {"format": "uri", "type": "string"}}}}, "properties": {"attributes": {"required": [], "type": "object", "description": "Attributes for describing a sample.", "patternProperties": {"^.*$": {"$ref": "#/definitions/attribute"}}, "properties": {}}}}, "description": "Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.", "properties": {"attributes": {"required": ["project name", "sequencing method", "investigation type", "collection date", "geographic location (country and/or sea)", "geographic location (latitude)", "geographic location (longitude)", "human skin environmental package", "environment (biome)", "environment (feature)", "environment (material)"], "properties": {"multiplex identifiers": {"description": "Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters", "items": {}}, "relationship to oxygen": {"description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments", "items": {"properties": {"value": {"enum": ["aerobe", "anaerobe", "facultative", "microaerophilic", "microanaerobe", "obligate aerobe", "obligate anaerobe"]}}}}, "host body temperature": {"description": "core body temperature of the host when sample was collected", "items": {"required": ["units"], "properties": {"value": {"pattern": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "host phenotype": {"description": "phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO", "items": {}}, "organism count": {"description": "total count of any organism per gram or volume of sample, should include name of organism followed by count; can include multiple organism counts", "items": {}}, "library vector": {"description": "Cloning vector type(s) used in construction of libraries", "items": {}}, "library screening strategy": {"description": "Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences", "items": {}}, "oxygenation status of sample": {"description": "oxygenation status of sample", "items": {"properties": {"value": {"enum": ["aerobic", "anaerobic"]}}}}, "ploidy": {"description": "The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2013-10-28) please refer to http://purl.bioontology.org/ontology/PATO. Mandatory for MIGS of eukaryotes.", "items": {}}, "dermatology disorder": {"description": "history of dermatology disorders; can include multiple disorders", "items": {}}, "observed biotic relationship": {"description": "Is it free-living or in a host and if the latter what type of relationship is observed", "items": {"properties": {"value": {"enum": ["commensal", "free living", "mutualism", "parasite", "symbiont"]}}}}, "temperature": {"description": "temperature of the sample at time of sampling", "items": {"required": ["units"], "properties": {"value": {"pattern": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "library reads sequenced": {"description": "Total number of clones sequenced from the library", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "host genotype": {"description": "observed genotype", "items": {}}, "source material identifiers": {"description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).", "items": {}}, "chemical administration": {"description": "list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI", "items": {}}, "known pathogenicity": {"description": "To what is the entity pathogenic, for instance plant, fungi, bacteria", "items": {}}, "host total mass": {"description": "total mass of the host at collection, the unit depends on host", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "geographic location (country and/or sea)": {"description": "The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).", "items": {"properties": {"value": {"enum": ["Afghanistan", "Albania", "Algeria", "American Samoa", "Andorra", "Angola", "Anguilla", "Antarctica", "Antigua and Barbuda", "Arctic Ocean", "Argentina", "Armenia", "Aruba", "Ashmore and Cartier Islands", "Atlantic Ocean", "Australia", "Austria", "Azerbaijan", "Bahamas", "Bahrain", "Baker Island", "Baltic Sea", "Bangladesh", "Barbados", "Bassas da India", "Belarus", "Belgium", "Belize", "Benin", "Bermuda", "Bhutan", "Bolivia", "Borneo", "Bosnia and Herzegovina", "Botswana", "Bouvet Island", "Brazil", "British Virgin Islands", "Brunei", "Bulgaria", "Burkina Faso", "Burundi", "Cambodia", "Cameroon", "Canada", "Cape Verde", "Cayman Islands", "Central African Republic", "Chad", "Chile", "China", "Christmas Island", "Clipperton Island", "Cocos Islands", "Colombia", "Comoros", "Cook Islands", "Coral Sea Islands", "Costa Rica", "Cote d'Ivoire", "Croatia", "Cuba", "Curacao", "Cyprus", "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", "Dominica", "Dominican Republic", "East Timor", "Ecuador", "Egypt", "El Salvador", "Equatorial Guinea", "Eritrea", "Estonia", "Ethiopia", "Europa Island", "Falkland Islands (Islas Malvinas)", "Faroe Islands", "Fiji", "Finland", "France", "French Guiana", "French Polynesia", "French Southern and Antarctic Lands", "Gabon", "Gambia", "Gaza Strip", "Georgia", "Germany", "Ghana", "Gibraltar", "Glorioso Islands", "Greece", "Greenland", "Grenada", "Guadeloupe", "Guam", "Guatemala", "Guernsey", "Guinea", "Guinea-Bissau", "Guyana", "Haiti", "Heard Island and McDonald Islands", "Honduras", "Hong Kong", "Howland Island", "Hungary", "Iceland", "India", "Indian Ocean", "Indonesia", "Iran", "Iraq", "Ireland", "Isle of Man", "Israel", "Italy", "Jamaica", "Jan Mayen", "Japan", "Jarvis Island", "Jersey", "Johnston Atoll", "Jordan", "Juan de Nova Island", "Kazakhstan", "Kenya", "Kerguelen Archipelago", "Kingman Reef", "Kiribati", "Kosovo", "Kuwait", "Kyrgyzstan", "Laos", "Latvia", "Lebanon", "Lesotho", "Liberia", "Libya", "Liechtenstein", "Lithuania", "Luxembourg", "Macau", "Macedonia", "Madagascar", "Malawi", "Malaysia", "Maldives", "Mali", "Malta", "Marshall Islands", "Martinique", "Mauritania", "Mauritius", "Mayotte", "Mediterranean Sea", "Mexico", "Micronesia", "Midway Islands", "Moldova", "Monaco", "Mongolia", "Montenegro", "Montserrat", "Morocco", "Mozambique", "Myanmar", "Namibia", "Nauru", "Navassa Island", "Nepal", "Netherlands", "New Caledonia", "New Zealand", "Nicaragua", "Niger", "Nigeria", "Niue", "Norfolk Island", "North Korea", "North Sea", "Northern Mariana Islands", "Norway", "Oman", "Pacific Ocean", "Pakistan", "Palau", "Palmyra Atoll", "Panama", "Papua New Guinea", "Paracel Islands", "Paraguay", "Peru", "Philippines", "Pitcairn Islands", "Poland", "Portugal", "Puerto Rico", "Qatar", "Republic of the Congo", "Reunion", "Romania", "Ross Sea", "Russia", "Rwanda", "Saint Helena", "Saint Kitts and Nevis", "Saint Lucia", "Saint Pierre and Miquelon", "Saint Vincent and the Grenadines", "Samoa", "San Marino", "Sao Tome and Principe", "Saudi Arabia", "Senegal", "Serbia", "Seychelles", "Sierra Leone", "Singapore", "Sint Maarten", "Slovakia", "Slovenia", "Solomon Islands", "Somalia", "South Africa", "South Georgia and the South Sandwich Islands", "South Korea", "Southern Ocean", "Spain", "Spratly Islands", "Sri Lanka", "Sudan", "Suriname", "Svalbard", "Swaziland", "Sweden", "Switzerland", "Syria", "Taiwan", "Tajikistan", "Tanzania", "Tasman Sea", "Thailand", "Togo", "Tokelau", "Tonga", "Trinidad and Tobago", "Tromelin Island", "Tunisia", "Turkey", "Turkmenistan", "Turks and Caicos Islands", "Tuvalu", "USA", "Uganda", "Ukraine", "United Arab Emirates", "United Kingdom", "Uruguay", "Uzbekistan", "Vanuatu", "Venezuela", "Viet Nam", "Virgin Islands", "Wake Island", "Wallis and Futuna", "West Bank", "Western Sahara", "Yemen", "Zambia", "Zimbabwe", "not applicable", "not collected", "not provided", "restricted access"]}}}}, "perturbation": {"description": "type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types", "items": {}}, "host body product": {"description": "substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA", "items": {}}, "environment (biome)": {"description": "Biomes are defined based on factors such as plant structures, leaf types, plant spacing, and other factors like climate. Biome should be treated as the descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO", "items": {}}, "host disease status": {"description": "list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text", "items": {}}, "environment (material)": {"description": "The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO", "items": {}}, "adapters": {"description": "Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters", "items": {}}, "IHMC medication code": {"description": "can include multiple medication codes", "items": {"properties": {"value": {"enum": ["01=1=Analgesics/NSAIDS", "02=2=Anesthetics", "03=3=Antacids/H2 antagonists", "04=4=Anti-acne", "05=5=Anti-asthma/bronchodilators", "06=6=Anti-cholesterol/Anti-hyperlipidemic", "07=7=Anti-coagulants", "08=8=Antibiotics/(anti)-infectives, parasitics, microbials", "09=9=Antidepressants/mood-altering drugs", "10=10=Antihistamines/ Decongestants", "11=11=Antihypertensives", "12=12=Cardiovascular, other than hyperlipidemic/HTN", "13=13=Contraceptives (oral, implant, injectable)", "14=14=Emergency/support medications", "15=15=Endocrine/Metabolic agents", "16=16=GI meds (anti-diarrheal, emetic, spasmodics)", "17=17=Herbal/homeopathic products", "18=18=Hormones/steroids", "19=19=OTC cold & flu", "20=20=Vaccine prophylaxis", "21=21=Vitamins, minerals, food supplements", "99=99=Other"]}}}}, "sample collection device or method": {"description": "The method or deviced employed for collecting the sample", "items": {}}, "sequencing method": {"description": "Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid", "items": {}}, "host family relationship": {"description": "relationships to other hosts in the same study; can include multiple relationships", "items": {}}, "pcr conditions": {"description": "Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'", "items": {}}, "host pulse": {"description": "resting pulse, measured as beats per minute", "items": {"required": ["units"], "properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "subspecific genetic lineage": {"description": "This should provide further information about the genetic distinctness of this lineage by recording additional information i.e biovar, serovar, serotype, biovar, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information", "items": {}}, "collection date": {"description": "The date of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.", "items": {"properties": {"value": {"pattern": "(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "propagation": {"description": "This field is specific to different taxa. For plants: sexual/asexual, for phages: lytic/lysogenic, for plasmids: incompatibility group (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice. Mandatory for MIGS of eukaryotes, plasmids and viruses.", "items": {}}, "project name": {"description": "Name of the project within which the sequencing was organized", "items": {}}, "relevant electronic resources": {"description": "-", "items": {}}, "sample storage temperature": {"description": "temperature at which sample was stored, e.g. -80", "items": {"required": ["units"], "properties": {"value": {"pattern": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "miscellaneous parameter": {"description": "Any other measurement performed or parameter collected, that is not listed here", "items": {}}, "host occupation": {"description": "most frequent job performed by subject", "items": {"properties": {"value": {"enum": ["01=01 Accounting/Finance", "02=02 Advertising/Public Relations", "03=03 Arts/Entertainment/Publishing", "04=04 Automotive", "05=05 Banking/ Mortgage", "06=06 Biotech", "07=07 Broadcast/Journalism", "08=08 Business Development", "09=09 Clerical/Administrative", "10=10 Construction/Trades", "11=11 Consultant", "12=12 Customer Services", "13=13 Design", "14=14 Education", "15=15 Engineering", "16=16 Entry Level", "17=17 Executive", "18=18 Food Service", "19=19 Government", "20=20 Grocery", "21=21 Healthcare", "22=22 Hospitality", "23=23 Human Resources", "24=24 Information Technology", "25=25 Insurance", "26=26 Law/Legal", "27=27 Management", "28=28 Manufacturing", "29=29 Marketing", "30=30 Pharmaceutical", "31=31 Professional Services", "32=32 Purchasing", "33=33 Quality Assurance (QA)", "34=34 Research", "35=35 Restaurant", "36=36 Retail", "37=37 Sales", "38=38 Science", "39=39 Security/Law Enforcement", "40=40 Shipping/Distribution", "41=41 Strategy", "42=42 Student", "43=43 Telecommunications", "44=44 Training", "45=45 Transportation", "46=46 Warehouse", "47=47 Other", "99=99 Unknown/Refused"]}}}}, "IHMC ethnicity": {"description": "ethnicity of the subject", "items": {}}, "host diet": {"description": "type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include multiple diet types", "items": {}}, "sample salinity": {"description": "salinity of sample, i.e. measure of total salt concentration", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "nucleic acid amplification": {"description": "Link to a literature reference, electronic resource or a standard operating procedure (SOP)", "items": {}}, "experimental factor": {"description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.43) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI", "items": {}}, "host height": {"description": "the height of subject", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "host last meal": {"description": "content of last meal and time since feeding; can include multiple values", "items": {}}, "investigation type": {"description": "Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardised by Genomic Standards Consortium", "items": {"properties": {"value": {"enum": ["bacteria_archaea", "eukaryote", "metagenome", "metagenome-assembled genome", "metatranscriptome", "mimarks-specimen", "mimarks-survey", "organelle", "plasmid", "single amplified genome", "uncultivated viral genomes", "virus"]}}}}, "target subfragment": {"description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA", "items": {}}, "library size": {"description": "Total number of clones in the library prepared for the project", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "reference for biomaterial": {"description": "Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.", "items": {}}, "library construction method": {"description": "Library construction method used for clone libraries", "items": {}}, "target gene": {"description": "Targeted gene or locus name for marker gene studies", "items": {}}, "host body-mass index": {"description": "body mass index, calculated as weight/(height)squared", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "amount or size of sample collected": {"description": "Amount or size of sample (volume, mass or area) that was collected", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "encoded traits": {"description": "Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage", "items": {}}, "trophic level": {"description": "Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)", "items": {"properties": {"value": {"enum": ["autotroph", "carboxydotroph", "chemoautotroph", "chemoheterotroph", "chemolithoautotroph", "chemolithotroph", "chemoorganoheterotroph", "chemoorganotroph", "chemosynthetic", "chemotroph", "copiotroph", "diazotroph", "facultative autotroph", "heterotroph", "lithoautotroph", "lithoheterotroph", "lithotroph", "methanotroph", "methylotroph", "mixotroph", "obligate chemoautolithotroph", "oligotroph", "organoheterotroph", "organotroph", "photoautotroph", "photoheterotroph", "photolithoautotroph", "photolithotroph", "photosynthetic", "phototroph"]}}}}, "isolation and growth condition": {"description": "Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.", "items": {}}, "pcr primers": {"description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters", "items": {}}, "geographic location (latitude)": {"description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", "items": {"required": ["units"], "properties": {"value": {"pattern": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "human skin environmental package": {"description": "MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", "items": {"properties": {"value": {"enum": ["human-skin"]}}}}, "dominant hand": {"description": "dominant hand of the subject", "items": {"properties": {"value": {"enum": ["ambidextrous", "left", "right"]}}}}, "medical history performed": {"description": "whether full medical history was collected", "items": {"properties": {"value": {"enum": ["No", "Yes"]}}}}, "host body site": {"description": "name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA", "items": {}}, "sample volume or weight for DNA extraction": {"description": "Volume (mL) or weight (g) of sample processed for DNA extraction", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "annotation source": {"description": "For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter", "items": {}}, "environment (feature)": {"description": "Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO", "items": {}}, "host sex": {"description": "Gender or sex of the host.", "items": {"properties": {"value": {"enum": ["female", "hermaphrodite", "male", "neuter", "not applicable", "not collected", "not provided", "other", "restricted access"]}}}}, "finishing strategy": {"description": "Was the genome project intended to produce a complete or draft genome, Coverage, the fold coverage of the sequencing expressed as 2x, 3x, 18x etc, and how many contigs were produced for the genome. Mandatory for MIGS of eukaryote, bacteria and archaea.", "items": {}}, "sequence quality check": {"description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA", "items": {"properties": {"value": {"enum": ["manual", "none", "software"]}}}}, "number of replicons": {"description": "Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "chimera check": {"description": "A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point", "items": {}}, "sample material processing": {"description": "Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI", "items": {}}, "time since last wash": {"description": "specification of the time since last wash", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "geographic location (longitude)": {"description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", "items": {"required": ["units"], "properties": {"value": {"pattern": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "estimated size": {"description": "The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "host age": {"description": "age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sample storage duration": {"description": "duration for which sample was stored", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "relevant standard operating procedures": {"description": "Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences", "items": {}}, "extrachromosomal elements": {"description": "Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "geographic location (region and locality)": {"description": "The geographical origin of the sample as defined by the specific region name followed by the locality name.", "items": {}}, "host subject id": {"description": "a unique identifier by which each subject can be referred to, de-identified, e.g. #131", "items": {}}, "sample storage location": {"description": "location at which sample was stored, usually name of a specific freezer/room", "items": {}}, "nucleic acid extraction": {"description": "Link to a literature reference, electronic resource or a standard operating procedure (SOP)", "items": {}}}}}, "required": ["attributes"], "id": "ERC000017", "type": "object", "title": "GSC MIxS human skin", "$schema": "http://json-schema.org/draft-07/schema#", "$async": true}, "_links": {"self": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000017"}, "checklist": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000017"}, "spreadsheet-csv-download": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000017/spreadsheet.csv"}}}